You're not seeing any performance loss from PCI-e bandwidth limitation unless you're in a very small slot (like PCI-e 2.0 x4). If you are on PCI-e 2.0 x8 or x16, you probably will see no benefit from going to PCI-e 3.0. Even the absolute fastest graphics cards out there see only a 1% benefit (at most) from moving from PCI-e 2.0 to PCI-e 3.0.
PCI Express 2.1 supports a large proportion of the management, support, and troubleshooting systems planned for full implementation in PCI Express 3.0. However, the speed is the same as PCI Express 2.0.